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comparison bowtie2_wrapper.xml @ 10:fed480fea9f0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author devteam
date Fri, 18 Dec 2015 18:50:22 -0500
parents aef49b7f08b2
children fa69d5a7b8c8
comparison
equal deleted inserted replaced
9:2ac3209cff00 10:fed480fea9f0
1 <tool id="bowtie2" name="Bowtie2" version="2.2.6"> 1 <tool id="bowtie2" name="Bowtie2" version="2.2.6.1">
2 <description>- map reads against reference genome</description> 2 <description>- map reads against reference genome</description>
3 <macros> 3 <macros>
4 <import>read_group_macros.xml</import> 4 <import>read_group_macros.xml</import>
5 </macros> 5 </macros>
6 <version_command>bowtie2 --version</version_command> 6 <version_command>bowtie2 --version</version_command>
163 --seed "${analysis_type.other_options.seed}" 163 --seed "${analysis_type.other_options.seed}"
164 #end if 164 #end if
165 165
166 #elif str( $analysis_type.analysis_type_selector ) == "cline": 166 #elif str( $analysis_type.analysis_type_selector ) == "cline":
167 ${analysis_type.cline} 167 ${analysis_type.cline}
168 #end if
169
170 ## mapping stats (i.e. stderr from bowtie2)
171 #if $save_mapping_stats
172 2&gt; "$mapping_stats"
168 #end if 173 #end if
169 174
170 ## output file 175 ## output file
171 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ): 176 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
172 | samtools view -Su - | samtools sort -o - - &gt; $output 177 | samtools view -Su - | samtools sort -o - - &gt; $output
428 </when> 433 </when>
429 </conditional> 434 </conditional>
430 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/> 435 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
431 </when> 436 </when>
432 </conditional> 437 </conditional>
438 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
433 </inputs> 439 </inputs>
434 440
435 <!-- define outputs --> 441 <!-- define outputs -->
436 442
437 <outputs> 443 <outputs>
514 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" /> 520 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
515 </action> 521 </action>
516 </when> 522 </when>
517 </conditional> 523 </conditional>
518 </actions> 524 </actions>
525 </data>
526 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
527 <filter>save_mapping_stats is True</filter>
519 </data> 528 </data>
520 529
521 </outputs> 530 </outputs>
522 531
523 <tests> 532 <tests>
548 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> 557 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
549 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> 558 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
550 <param name="own_file" value="bowtie2-ref.fasta" /> 559 <param name="own_file" value="bowtie2-ref.fasta" />
551 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/> 560 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
552 </test> 561 </test>
562 <test>
563 <!-- basic test on single paired default run with stats-->
564 <param name="type" value="paired"/>
565 <param name="selection" value="no"/>
566 <param name="paired_options_selector" value="no"/>
567 <param name="unaligned_file" value="false"/>
568 <param name="analysis_type_selector" value="simple"/>
569 <param name="source" value="history" />
570 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
571 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
572 <param name="own_file" value="bowtie2-ref.fasta" />
573 <param name="save_mapping_stats" value="true" />
574 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
575 <output name="mapping_stats" file="bowtie2-stats.out" ftype="txt"/>
576 </test>
553 </tests> 577 </tests>
554 578
555 <help> 579 <help>
556 580
557 **Bowtie2 Overview** 581 **Bowtie2 Overview**